Fiehn Lab - Publications

Papers

Hiroshi Tsugawa, Tomas Cajka, Tobias Kind, Yan Ma, Brendan Higgins, Kazutaka Ikeda, Mitsuhiro Kanazawa, Jean VanderGheynst, Oliver Fiehn & Masanori Arita; MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis; Nature Methods (2015) ASAP doi:10.1038/nmeth.3393 [LINK] [Software]

Y Ma, T Kind, D Yang, C Leon, O Fiehn; MS2Analyzer: A Software for Small Molecule Substructure Annotations from Accurate Tandem Mass Spectra; Analytical chemistry 86 (21), 10724-10731 [LINK]

T Kind, Y Okazaki, K Saito, O Fiehn; LipidBlast templates as flexible tools for creating new in-silico tandem mass spectral libraries;Analytical chemistry 86 (22), 11024-11027 [LINK]

Do Yup Lee, Tobias Kind, Young-Ran Yoon, Oliver Fiehn, Kwang-Hyeon Liu Comparative evaluation of extraction methods for simultaneous mass-spectrometric analysis of complex lipids and primary metabolites from human blood plasma; Analytical and bioanalytical chemistry (2014) ASAP; DOI:10.1080/09168451.2014.877826 [LINK]

Takumi Ogawa, Takeshi Furuhashi, Atsushi Okazawa, Rai Nakai, Masami Nakazawa, Tobias Kind, Oliver Fiehn, Shigehiko Kanaya, Masanori Arita, Daisaku Ohta Exploration of polar lipid accumulation profiles in Euglena gracilis using LipidBlast, an MS/MS spectral library constructed in silico; Bioscience, Biotechnology, and Biochemistry (2014) ASAP; DOI:10.1080/09168451.2014.877826 [LINK]

Tobias Kind, Kwang-Hyeon Liu, Do Yup Lee, Brian DeFelice, John K Meissen & Oliver Fiehn LipidBlast in silico tandem mass spectrometry database for lipid identification. Nature Methods (2013) Aug;10(8):755-8; DOI: http://dx.doi.org/10.1038/nmeth.2551 [LINK]

Sean F Gilmore, Andrew I Yao, Zipora Tietel, Tobias Kind et al. Role of Squalene in the Organization of Monolayers Derived from Lipid Extracts of Halobacterium salinarum. In Langmuir : ACS journal of surfaces and colloids 29 (25). 7922-30. (2013)http://dx.doi.org/10.1021/la401412t

D Yang, Fan XL, Kind T et al. (2013) Analysis of Polar Lipids in Chlamydomonas reinhardtii Using Nanoelectrospray Direct Infusion Method and Gas Chromatography and Mass Spectrometric Detection, 663-669. In ACTA CHIMICA SINICA 71 (4). http://dx.doi.org/10.6023/A13010152

John K. Meissen , Benjamin Yuen, Tobias Kind, John W. Riggs, Dinesh K. Barupal, Paul S.Knoepfler and Oliver Fiehn Induced pluripotent stem cells show metabolomic differences to embryonic stem cells in polyunsaturated phosphatidylcholines and primary metabolism PLoS ONE 2012, 7(10): e46770. doi:10.1371/journal.pone.0046770

Peggy P. Ho, Jennifer L. Kanter, Amanda M. Johnson, Hrishikesh K. Srinagesh, Eun-Ju Chang, Timothy M. Purdy, Keith van Haren, William R. Wikoff, Tobias Kind, Mohsen Khademi, Laura Y. Matloff, Sirisha Narayana, Eun Mi Hur, Tamsin M. Lindstrom, Zhigang He, Oliver Fiehn, Tomas Olsson, Xianlin Han, May H. Han, Lawrence Steinman, William H. Robinson Identification of naturally occurring fatty acids of the myelin sheath that resolve neuroinflammation; Science Translational Medicine 4, 137ra73 (2012). [DOI]

Dinesh K Barupal, Pradeep K Haldiya, Gert Wohlgemuth, Tobias Kind, Shanker L Kothari, Kent E Pinkerton and Oliver Fiehn MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity BMC Bioinformatics 2012, 13:99. [LINK] [MetaMapp Server] [Blog about MetaMapp]

Im-Sook Song, Do Yup Lee, Min-Hye Shin, Hyunmi Kim, Yun Gyong Ahn, Inmyoung Park, Kyoung Heon Kim, Tobias Kind, Jae-Gook Shin, Oliver Fiehn, Kwang-Hyeon Liu Pharmacogenetics Meets Metabolomics: Discovery of Tryptophan as a New Endogenous OCT2 Substrate Related to Metformin Disposition; PLoS ONE 7(5): e36637. (2012) doi:10.1371/journal.pone.0036637 [Link]

Tobias Kind, John K. Meissen, Dawei Yang, Fernando Nocito, Arpana Vaniya, Yu-Shen Cheng, Jean S. VanderGheynst, Oliver Fiehn Qualitative analysis of algal secretions with multiple mass spectrometric platforms Journal of Chromatography A (2012); ASAP Available online 4 May 2012; doi: 10.1016/j.chroma.2012.04.074 [DOI] [PDF]

Sangeeta Kumari , Doug Stevens , Tobias Kind , Carsten Denkert , and Oliver Fiehn Applying in-silico retention index and mass spectra matching for identification of unknown metabolites in accurate mass GC-TOF mass spectrometry Analytical Chemistry June 2011, ASAP, DOI: 10.1021/ac2006137, [LINK]

Oliver Fiehn, Dinesh K. Barupal, Tobias Kind; EXTENDING BIOCHEMICAL DATABASES BY METABOLOMIC SURVEYS J. Biol. Chem. , 2011, jbc.R110.173617., [LINK]

Buckendahl AC, Budczies J, Fiehn O, Darb-Esfahani S, Kind T, Noske A, Weichert W, Sehouli J, Braicu E, Dietel M, Denkert C. Prognostic impact of AMP-activated protein kinase expression in ovarian carcinoma: Correlation of protein expression and GC/TOF-MS-based metabolomics. Oncol Rep. 2011 Apr;25(4):1005-12. doi: 10.3892/or.2011.1162. Epub 2011 Jan 25. [PDF]

Oliver Fiehn, Tobias Kind and Dinesh Kumar Barupal Data Processing, Metabolomic Databases and Pathway Analysis Annual Plant Reviews (2011) 43, 367-406; doi: 10.1002/9781405199544.ch12 [OCLC] [LINK] Chapter in ANNUAL PLANT REVIEWS VOLUME 43; Biology of Plant Metabolomics; Edited by Robert Hall; Wiley-Blackwell

Wohlgemuth G., Haldya P.K., Willighagen E.L., Kind T.; Fiehn O. The Chemical Translation Service (CTS) – a web-based tool to improve standardization of metabolomic reports Bioinformatics (Oxford) 2010, doi:10.1093/bioinformatics/btq476 [LINK] [Google Code] [CTS]

Tobias Kind and Oliver Fiehn Advances in Structure Elucidation of Small Molecules Using Mass Spectrometry Bioanalytical Reviews, Volume 2, Issue 1, 2010, Pages 23-60, doi:10.1007/s12566-010-0015-9 [LINK] [PDF] [HTML] [OA-PDF]

Dinesh K Barupal, Tobias Kind, Shankar L Kothari, Do Yup Lee and Oliver Fiehn Hydrocarbon phenotyping of algal species using pyrolysis-gas chromatography mass spectrometry BMC Biotechnology 2010, 10:40 doi:10.1186/1472-6750-10-40 [LINK] [PDF]

Salvatore Abate, Yun Gyong Ahn, Tobias Kind, Tommaso R. I. Cataldi, Oliver Fiehn Determination of elemental compositions by gas chromatography/time-of-flight mass spectrometry using chemical and electron ionization Rapid Communications in Mass Spectrometry 2010; Volume 24, Issue 8, Pages 1172-1180 [LINK] [DOI]

Tobias Kind, Oliver Fiehn What are the obstacles for an integrated system for comprehensive interpretation of cross-platform metabolic profile data? Bioanalysis, December 2009, Vol. 1, No. 9, Pages 1511-1514.; [LINK] [PDF]

Kind, Tobias; Wohlgemuth, Gert; Lee, Do Yup; Lu, Yun; Palazoglu, Mine; Shahbaz, Sevini; Fiehn, Oliver FiehnLib – mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry. Anal. Chem., 2009, 81 (24), pp 10038-10048; DOI: 10.1021/ac9019522 [LINK] [Project Website]

Kind T, Leamy T, Leary JA, Fiehn O Software platform virtualization in chemistry research and university teaching. Journal of Cheminformatics 2009, 1:18 doi:10.1186/1758-2946-1-18 [LINK] [PDF] [PREPRINT] [XLS]

Kind T, Scholz M, Fiehn O How Large Is the Metabolome? A Critical Analysis of Data Exchange Practices in Chemistry. PLoS ONE 4(5): e5440. (2009); doi:10.1371/journal.pone.0005440 [LINK]

Carsten Denkert, Jan Budczies, Wilko Weichert, Gert Wohlgemuth, Martin Scholz, Tobias Kind, Silvia Niesporek, Aurelia Noske, Anna Buckendahl, Manfred Dietel, Oliver Fiehn Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover; Molecular Cancer 2008, 7:72; [LINK]

Kind, T., Fiehn, O., Hardware and software challenges for the near future: Structure elucidation concepts via hyphenated chromatographic techniques, IN: MS-Practical Art, Balogh, M.P. (ed.), LC-GC North America 26, 176-187 (2008). [LINK]

Fiehn O, Wohlgemuth G, Scholz M, Kind T, Lee DY, Lu Y, Moon S, Nikolau BJ Quality control for plant metabolomics: Reporting MSI-compliant studies. Plant Journal (2008) 53, 691-704 [LINK]

Kind, T Instant-JChem CHEMISTRY WORLD, 4 (11): 68-68 NOV 2007 [LINK]

Kind, T; Fiehn, O Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry BMC BIOINFORMATICS, 8: Art. No. 105 MAR 27 2007 [LINK] [PDF]

Kind, T; Tolstikov, V; Fiehn, O; et al. A comprehensive urinary metabolomic approach for identifying kidney cancer ANALYTICAL BIOCHEMISTRY, 363 (2): 185-195 APR 15 2007 [LINK]

Denkert, C; Budczies, J; Kind, T; et al. Mass spectrometry-based metabolic profiling reveals different metabolite patterns in invasive ovarian carcinomas and ovarian borderline tumors CANCER RESEARCH, 66 (22): 10795-10804 NOV 15 2006 [LINK]

Fiehn O, Kind T (2006) Metabolite profiling in blood plasma. In: Metabolomics: Methods and Protocols. Weckwerth W (ed.), Humana Press, Totowa NJ, ISBN13: 978-1-59745-244-1. Methods in Molecular Biology 358, 3-18 [LINK]

Kind, T; Fiehn, O Metabolomic database annotations via query of elemental compositions: Mass accuracy is insufficient even at less than 1 ppm; BMC BIOINFORMATICS, 7: Art. No. 234 APR 28 2006 [LINK] [PDF]

Eckel, WP; Kind, T; Use of boiling point-Lee retention index correlation for rapid review of gas chromatography-mass spectrometry data; ANALYTICA CHIMICA ACTA, 494 (1-2): 235-243 OCT 8 2003 [LINK]

Brack, W; Kind, T; Hollert, H; et al.; Sequential fractionation procedure for the identification of potentially cytochrome P4501A-inducing compounds; JOURNAL OF CHROMATOGRAPHY A, 986 (1): 55-66 JAN 31 2003 [LINK]

Brack, W; Kind, T; Schrader, S; et al.; Polychlorinated naphthalenes in sediments from the industrial region of Bitterfeld;ENVIRONMENTAL POLLUTION, 121 (1): 81-85 2003 [LINK]

Brack, W; Schirmer, K; Kind, T; et al.; Effect-directed fractionation and identification of cytochrome P4501A-inducing halogenated aromatic hydrocarbons in a contaminated sediment; ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY, 21 (12): 2654-2662 DEC 2002 [LINK]

Conferences, talks and posters

2015, West Coast Metabolomics Center Seminar, Davis, USA; CRISPR/Cas9 for advanced DNA and RNA editing; Tobias Kind; [DOI: 10.13140/2.1.3517.0083] [PDF]

2014, 10th International Conference of the Metabolomics Society, Tsuruoka, Japan; MS DIAL: Untargeted metabolomics software for data independent LC-MS/MS and mass spectral deconvolution: application to algae metabolomics; Hiroshi Tsugawa; Tobias Kind; Tomas Cajka; Yan Ma; Kazutaka Ikeda; Mitsuhiro Kanazawa; Atsushi Ogiwara; Oliver Fiehn; Masanori Arita;

2014, 10th International Conference of the Metabolomics Society, Tsuruoka, Japan; Role of co-factors in alleviating metabolic bottlenecks for mixotrophic production of algal biofuels Brendan Thomas Higgins; Jean VanderGheynst; Tobias Kind; Oliver Fiehn;

ASMS 2014 - 62nd ASMS Conference on Mass Spectrometry and Allied Topics, Baltimore, MD Structural Characterization and Fragmentation Rule Generation of Flavonoids Using Fragmentation TreesArpana Vaniya; Yan Ma; Tobias Kind; Oliver Fiehn

ASMS 2014 - 62nd ASMS Conference on Mass Spectrometry and Allied Topics, Baltimore, MD Retention 'Projection' Enables Reliable Use of Shared HPLC Metabolite Retention Data Across Labs and MethodsDaniel Abate-Pella; Dana Freund; Yan Ma; Birgit Beck; Emma Schymanski; Tobias Kind; Adrian Hegeman; Paul Boswell

2013 NIH West Coast Metabolomics Center, Seminar in Metabolomics, Davis, CA Metabolite identifications with virtual mass spectral libraries Tobias Kind

2013 NSF-JST Joint Workshop "Metabolomics for Low carbon Society" Nara, Japan Annotation of unknown compounds in algae using tandem mass spectra Tobias Kind, Yan Ma, Oliver Fiehn

2013 RIKEN CSRS Workshop: Metabolomics to Better Understand Plant Specialized Metabolism, Yokohama, Japan METABOLOMICS: Integrating cheminformatic resources for investigating photoautotrophic and mixotrophic metabolism in algaeOliver Fiehn, Tobias Kind

ASMS 2013 - 61st ASMS Conference on Mass Spectrometry and Allied Topics. Minneapolis, Minnesota Automated Tool for Substructure Annotation of Accurate Mass MS/MS Spectra Yan Ma; Tobias Kind; Oliver Fiehn; University of California, Davis, CA

2013 Conference on Small Molecule Science (CoSMoS) Meeting San Diego 2013 How can we get data for “all metabolites” in Chlamydomonas reinhardtii ? Nutan Kaushik , Tobias Kind, William Wikoff,Zipora Tietel, Oliver Fiehn

2012 UC Davis Biotechnology Program - Davis, CA (invited talk) Machine learning applications in biotechnology research Tobias Kind [PDF]

ASMS 2012 - 60TH ASMS Conference on Mass Spectrometry and Allied Topics, Vancouver, Canada Integration of Multiple Mass Spectrometry Based Techniques for Enhanced Coverage in Metabolite Profiling of Stem Cells John Meissen; Benjamin Yuen; Tobias Kind; John Riggs; Dinesh Barupal; Paul Knoepfler; Oliver Fiehn; UC Davis, Davis, CA

American Diabetes Association’s 72nd Scientific Sessions, June 8-12, 2012 in Philadelphia, PA. (abstract accepted)Effects of Polyunsaturated Fatty Acids (PUFA) on Glucose Homeostasis May Be Mediated Through Changes in Amino Acid Metabolites, Karakas SE; Fiehn O; Kind T; Perroud B; Palazoglu M

2011 PhD Summer School - Aarhus University Denmark (invited virtual talk) Structure elucidation of small molecules utilizing tandem mass spectrometry Tobias Kind

3rd Annual Algae World Summit 2011 - San Diego, CA (invited talk) Lipid and metabolic profiling of algae under environmental stressTobias Kind [Agenda PDF]

ASMS 2011 - 59th ASMS Conference on Mass Spectrometry; Denver, Colorado De novo identification of small molecules with computer generated MS/MS libraries Tobias Kind and Oliver Fiehn [Link]

ASMS 2011 - 59th ASMS Conference on Mass Spectrometry; Denver, Colorado Accurate Mass HILIC-MS/MS for Metabolomics Analysis of Blood Plasma John Meissen; Massud Atta; Kevin Siek; Alessio Ceroni; Tobias Kind; Oliver Fiehn [Link]

ASMS 2011 - 59th ASMS Conference on Mass Spectrometry; Denver, Colorado Retention index as Filter for Molecular Formulas in Derivatization Based GC-MS Sangeeta Kumari; Tobias Kind; Oliver Fiehn [Link]

PITTCON Conference 2011 - Atlanta, Georgia, USA Towards a Standardized Metabolomics Repository Fiehn O; Wohlgemuth G; Kind T. [PDF] [LINK]

2011 First Annual Berkeley Metabolomics Symposium - Lawrence Berkeley National Laboratory, CA (talk) Computational methods for metabolomics, Tobias Kind [LINK]

2010, 4th Central and Eastern European Proteomics Conference meets International Metabolomics Austria, Vienna, Austria PERSPECTIVES OF METABOLOMICS TOWARDS PERSONALIZED MEDICINE Oliver Fiehn, Carsten Denkert, Dinesh K. Barupal, Gert Wohlgemuth, Tobias Kind; [PDF]

2010 UC Davis Bioinformatics Technology Forum (talk) Charting unknown territories – reverse QSARs, random forests, in-silico spectra – and the hunt for the holy grail in mass spectrometry, Tobias Kind [LINK]

2010 Metabolomics Society Conference - Amsterdam, The Netherlands Chemical Translation Service – a database approach to standardize conversion of chemical identifiers Gert Wohlgemuth, Praedeep Haldiya, Tobias Kind, Oliver Fiehn [PDF]

2010 Metabolomics Society Conference - Amsterdam, The Netherlands Annotation of unknown metabolites in breast cancer samples using accurate mass GC-TOF MS and substructure features [PDF] Sangeeta Kumari, Doug Stevens, Carsten Denkert, Tobias Kind, Oliver Fiehn

2010 Stanford University Mass Spectrometry (SUMS) - Metabolomics User Group Meeting (talk) Structure elucidation approaches for metabolic profiling and biomarker studies using mass spectrometry Tobias Kind

ASMS 2010 - 58th ASMS Conference on Mass Spectrometry; Salt Lake City, Utah (short talk) (short talk - ASMS Flavor and Fragrance Workshop) GC-TOF applications of accurate mass measurements Tobias Kind, Kirsten Skogerson, Sangeeta Kumari, Doug Stevens, Oliver Fiehn [PDF]

ASMS 2010 - 58th ASMS Conference on Mass Spectrometry; Salt Lake City, Utah Hydrocarbon phenotyping of algal species using pyrolysis gas chromatography mass spectrometry Dinesh Kumar; Tobias Kind; Oliver Fiehn ASMS 2010 - 58th ASMS Conference on Mass Spectrometry; Salt Lake City, Utah Lipid identification using a MS/MS database of 120,000 tandem mass spectra Tobias Kind; Kwang-Hyeon Liu; Do Yup Lee; Oliver Fiehn

ASMS 2010 - 58th ASMS Conference on Mass Spectrometry; Salt Lake City, Utah Identification of unknown metabolites by accurate mass GC-TOF MS based metabolomics Sangeeta Kumari; Doug Stevens; Tobias Kind; Oliver Fiehn

American Chemical Society - National Meeting 239, San Francisco, Spring, 2010 (invited talk) Generation of in-silico MS/MS mass spectra using combinatorial algorithms and reaction prediction expert systemsT. Kind, K.-H. Liu, D. Y. Lee, O. Fiehn [LINK] [PDF]

ABRF 2010 Meeting - Association of Biomolecular Resource Facilities, Sacramento, CA Managing Complexity - How Many Platforms do We Need for Metabolomics? O. Fiehn, T. Kind, G. Wohlgemuth, M. Palazoglu, D.K. Barupal, S. Shahbaz [LINK] ASMS 2009 - 57th ASMS Conference on Mass Spectrometry; Philadelphia, Pennsylvania Metabolic signatures of human drug response phenotyping Oliver Fiehn; Gert Wohlgemuth; Dinesh Kumar Barupal; Tobias Kind; Rima Kaddurah-Daouk

Metabolomics Society Conference 2009 - Edmonton, Alberta, Canada Lipidomic changes in hepatic lipase knockout mice revealed by chip-based direct infusion nanoelectrospray ion trap mass spectrometry Kwang-Hyeon Liu, Serena M Pratt, Saeed Khazaie, Do Yup Lee, Tobias Kind, Jens Hoefken, Craig Warden, and Oliver Fiehn [PDF]

Metabolomics Society Conference 2009 - Edmonton, Alberta, Canada Lipid identification by tandem mass spectrometry using an in-silico generated fragment database Tobias Kind, Kwang-Hyeon Liu, Do Yup Lee, Oliver Fiehn

ChemAxon 2009 US User Group Meeting, San Diego, CA (session talk) Cheminformatics approaches for metabolomics Tobias Kind, UC Davis Genome Center [PDF] [WEB]

PITTCON Conference 2009, Chicago (invited session talk) Compound identification in GC-MS based metabolomics. Tobias Kind and Oliver Fiehn; UC Davis Genome Center - Metabolomics

Conference: Metabolomics Society Meeting 2008, Boston (session talk) Annotation of unknown metabolites with accurate mass LC-MS/MS and GC-MS by constraining metabolite database queries using analytical metadata Tobias Kind, UC Davis Genome Center

Conference: Metabolomics Society Meeting 2008, Boston Mapping metabolic alterations in rat lungs and blood plasma Dinesh Kumar, Tobias Kind, Carol Hood, Jesse Joad, Kent Pinkerton, Oliver Fiehn UC Davis - Metabolomics, Davis, CA [PDF]

Conference: Metabolomics Society Meeting 2008, Boston Plasma Lipid Profiling Using Chip-Based Direct Infusion Nanospray Tandem Mass Spectrometry Kwang-Hyeon Liu, Do Yup Lee, Tobias Kind, and Oliver Fiehn

COSMOS Small Molecule Science Conference 2008, San Jose CA (session talk) Using GC-MS, LC-MS and FT-ICR-MS Data for Structure Elucidation of Small Molecules Tobias Kind; UC Davis Genome Center - Metabolomics [LINK] [PDF]

American Society for Mass Spectrometry - ASMS Conference 2008 Denver (session talk) Structural annotation of small molecules by mass spectral libraries, substructure information and accurate mass GC-MS data TOBIAS KIND; Gert Wohlgemuth; Yun Lu; Mine Palazoglu; Martin Scholz; Oliver Fiehn; UC Davis - Metabolomics, Davis, CA [PDF]

ASMS Conference 2008, Denver USA Biochemical Mapping of Metabolic Alterations in Lungs of Rat Embryos; OLIVER FIEHN; Dinesh Kumar; Gert Wohlgemuth; Jesse Joad; Carol Hood; Kent Pinkerton; Tobias Kind; UC Davis, Davis, CA [PDF]

ASMS Conference 2008, Denver USA Mapping of Chemical and Biochemical Relationships of Mass Spectrometry-based Metabolomics Data Dinesh Kumar; Tobias Kind; OLIVER FIEHN; UC Davis, Davis, CA [PDF]

ASMS Conference 2008, Denver USA An automated workflow for rapid alignment and identification of lipid biomarkers obtained from chip-based direct infusion nanoelectrospray tandem mass spectrometry; Jens Hoefkens (1); TOBIAS KIND (2); Kent Pinkerton (3); Oliver Fiehn (2); (1) Genedata Inc, Waltham, MA; (2) UC Davis - Metabolomics, Davis, CA; (3) UC Davis Center for Health and the Environment, Davis, CA [PDF]

98th AACR Annual Meeting-- Apr 14-18, 2007; Los Angeles, CA GC-TOF based metabolic profiling of human colon carcinoma; Carsten Denkert, Jan Budczies, Wilko Weichert, Tobias Kind, Silvia Niesporek, Aurelia Noske, Anna Buckendahl, Manfred Dietel and Oliver Fiehn [LINK]

ASMS Conference 2007, Indianapolis USA; A machine learning pipeline for substructure detection in unknown mass spectra; Tobias Kind; Oliver Fiehn; UC Davis - Metabolomics, Davis, CA [PDF]

ASMS Conference 2006, Seattle USA; Profiling of Urinary Metabolites; Vladimir V. Tolstikov, Tobias Kind, Kindra D. Brooks, Robert H. Weiss; UC Davis - Metabolomics, Davis, CA [PDF]

ASMS Conference 2005, San Antonio USA; High quality plant metabolomics by GC-TOF mass spectrometry and automated database annotation: 1000 runs * 500 metabolites; Oliver Fiehn; Tobias Kind; Gert Wohlgemuth; UC Davis Genome Center, Davis, CA [PDF]

ASMS Conference 2005, San Antonio USA; Automated two step derivatization coupled to Direct-Thermal-Desorption GC-TOF-MS;Tobias Kind (1); Oliver Lerch (2); Peter Tablack (3); Carsten Denkert (4); Oliver Fiehn (1); (1) UC Davis Genome Center, Davis, CA; (2) Gerstel GmbH, Mülheim an der Ruhr, Germany; (3) Leco GmbH, Mönchengladbach, Germany; 4-Institute of Pathology, Humboldt University, Berlin, Germany; [PDF]

ASMS 2005 Conference, San Antonio USA (talk - metabolomics user group meeting); Metabolomic Workflows: Integrating Biological and MS Metadata; Tobias Kind; Martin Scholz; Gert Wohlgemuth; Oliver Fiehn; UC Davis Genome Center, Davis, CA

SETAC World Congress 2000, Brighton, UK (session talk); Fractionation and chemical analysis of watercourse SPMD extracts; Kind, Tobias, Vrana, Brano, Brack, Werner, Schüürmann, Gerrit; UFZ Centre for Environmental Research Halle Leipzig [PDF]

Reviewer for journals and grants

Nature Methods (Nature)

Nature Scientific Reports (Nature)

Nature Communications

Angewandte Chemie (Wiley)

Plant Physiology (ASPB)

Analytical Chemistry (ACS)

Journal of Proteome Research (ACS)

Molecular and Cellular Proteomics (ASBMB)

Grant Agency of the Academy of Sciences (Czech Republic)

NSF EPSCoR (Mississippi State Univ)

University of Maryland and the U.S. Department of Agriculture (US)

American Association for the Advancement of Science (AAAS)

INRA (National Institute of Agricultural Research) (France)

PLOS One (The Public Library of Science)

Genome Medicine (BMC/Springer SBM)

BMC Bioinformatics (Springer)

Bioinformatics (Oxford Journals)

Metabolomics (Springer)

Current Metabolomics (Bentham)

Journal of Chromatography A (Elsevier)

Journal of Chromatography B (Elsevier)

QSAR & Combinatorial Science (Wiley VCH)

Journal of Chemical Information and Modeling (ACS)

Journal of Computer-Aided Molecular Design (Springer)

Rapid Communications in Mass Spectrometry (Wiley)

Journal of The American Society for Mass Spectrometry (Springer)

Journal of Mass Spectrometry (Wiley)

Analytica Chima Acta (Elsevier)

Croatica chemica acta (The Croatian Chemical Society)

Clinica Chimica Acta (Elsevier)

BMC Gastroenterology (BioMed Central)

Pharmacogenomics (Future Medicine)

BMC Physiology (Biomed Central/Springer)

Metabolites (MDPI) Marine Drugs (MDPI)

International Journal of Molecular Sciences (MDPI)

Journal of Pharmaceutical and Biomedical Analysis (Elsevier)

Chemometrics and Intelligent Laboratory Systems (Elsevier)

Journal of Cheminformatics (BMC/Springer SBM)

Bioanalysis (Future Medicine)

Computers & Education (Elsevier)

Computational and Structural Biotechnology Journal (RNCSB)

Recent Advances in Phytochemistry (Phytochemical Society of North America)

Phytochchemical Analysis (Wiley)

Nucleic Acids Research (Oxford)

Trends in Analytical Chemistry TrAC (Elsevier)

Analytical Methods (RSC)

Analyst (RSC)

Electrophoresis (Wiley/VCH)

Algal Research (Elsevier)

Journal of Agricultural and Food Chemistry (ACS)

Molecular Phenomics (Nature)

Forensic Sciences Research (Taylor & Francis)

PI or Co-PI in grants

UCMEXUS 2011 - Tobias Kind and Oliver Fiehn, Genome Center-Metabolomics, UC Davis and Eugenia Lugo-Cervantes, Tecnología Alimentaria, CIATEJ; Isolation and characterization of saponins from Agave durangensis and salmiana and their effect on cell membrane of Kluyveromyces marxianus and Saccharomyces cerevisiae yeast in a fermentation process; Aislamiento y caracterización de las saponinas de Agave durangensis y salmiana y el efecto sobre la membrana de Kluyveromyces marxianus y Saccharomyces cerevisiae en el proceso de fermentación [LINK]

NSF 2011 - Metabolomics for a Low Carbon Society; Research led by Oliver Fiehn of the University of California at Davis and Masanori Arita of the University of Tokyo. This project will improve methods to identify metabolites used by photosynthetic algae to produce biofuel--information that will be used to boost the manufacturing of biofuel. Project activities include advancing techniques in mass spectrometry--a method used to estimate the mass of molecules--and developing a new, integrated mass spectrometry database that will be freely accessible to the research community.

NSF 2014 - Managing mixotrophic algae cultivation for efficient water treatment and biofuel production; Research led by Jean VanderGheynst, Oliver Fiehn, Tobias Kind and Brendan Higgins to develop algae cultivation and wastewater management systems that lead to higher substrate utilization efficiencies for biofuel production and organic matter removal from wastewater. Management options include strain selection and algae acclimation, rate and timing of substrate addition and management of wastewater composition. An additional goal is to determine bottlenecks in substrate utilization by microalgae. The first objective is to determine if acclimation of microalgae to organic carbon reduces substrate utilization efficiency and develop strategies to overcome this challenge. The second objective is to vary organic carbon and co-factor addition to algae using fed-batch reactors to determine if substrate supply rate impacts conversion efficiency, and the third objective is to use results from objectives 1 and 2 to tailor microalgae production variables for cultivation on food processing wastewaters.

AHA 2015- American Heart Association; Genomics of Lipidomic Phenotypes in a Postprandial Intervention Dietary Study (PI: Marguerite Ryan Irvin); (Role: co-PI) This proposal is led by Dr. Ryan Irvin, University of Alabama at Birmingham together with co-PI Dr. Kind at the UC Davis Genome Center and NIH West Coast Metabolomics Center. The study is based on research from a large and well-characterized family study, the Genetics of Lipid Lowering and Diet Network (GOLDN) and the HAPI Heart cohort. The proposal plans to link genetic with metabolic and lipidomic information to understand dyslipidemia (the abnormal elevation of lipids) and associated cardiovascular diseases. For that purpose lipidomics and steroid profiles will be measured at the West Coast Metabolomics Center in tight coordination with the director of the West Coast Metabolomics Center, Prof. Dr. Oliver Fiehn.

NIH 2015 - NIH/NHLBI; Genomewide Association Study of Lipid Response to Fenofibrate and Dietary Fat (PI: Arnett, Donna K.); Excerpt: Recent advances in mass spectrometry-based techniques allow metabolomic characterization in large populations. Detailed and precise measurement of lipid molecular species, a field known as "lipidomics," now offers an unprecedented picture of lipid metabolism. The Genetics of Lipid-Lowering Drugs and Diet Network (GOLDN) Study provides an ideal context in which to pursue this work. GOLDN is the largest family study conducted to date that has sought to identify genetic factors that explain response to two short-term interventions, one to raise lipids (i.e., ingestion of a high-fat meal, the "post-prandial lipemia" (PPL) intervention and one to lower lipids (i.e., treatment with fenofibrate (FFB)). The goal of the "Genomewide Association Study (GWAS) of Lipid Response to Fenofibrate and Dietary Fat" (Arnett, PI, R01-HL091357) was to identify the common genetic variants that explain response to the interventions. In addition to this, GOLDN is also conducting a genome- wide epigenomics study and exome sequencing through the NIH Pharmacogenomics Research Network (PGRN). The proposed work will leverage this wealth of genomic data in the context of state-of-the-art lipidomic phenotypes, specifically phospholipids, neutral lipids, and sterols, to identify rare and common variants and epigenetic marks that determine response to GOLDN's diet and drug interventions.